VEP run statistics
| VEP version (API) | 113.0 (113) |
| Annotation sources | Cache: /tmp/nxf.XXXXYVNY6n/113_GRCh38/homo_sapiens/113_GRCh38 |
| Species | homo_sapiens |
| Command line options | --assembly GRCh38 --cache --cache_version 113 --compress_output bgzip --dir_cache /tmp/nxf.XXXXYVNY6n/113_GRCh38 --everything --filter_common --fork 4 --format vcf --input_file 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.whatshap.phased_custom.ann_snpEff.ann.vcf.gz --offline --output_file 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann.vcf.gz --per_gene --species homo_sapiens --stats_file 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann.summary.html --total_length --vcf |
| Start time | 2026-02-03 06:45:19 |
| End time | 2026-02-03 06:46:04 |
| Run time | 45 seconds |
| Input file | 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.whatshap.phased_custom.ann_snpEff.ann.vcf.gz |
| Output file | 1029_BICA-T1-TDNA-1_23FC2GLT4_s33_vs_1029_BICA-N1-BDNA-1_2375WFLT3_s32.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann.vcf.gz |
Data version
| 1000genomes | phase3 |
| COSMIC | 99 |
| ClinVar | 202404 |
| HGMD-PUBLIC | 20204 |
| assembly | GRCh38.p14 |
| dbSNP | 156 |
| gencode | GENCODE 47 |
| genebuild | GENCODE47 |
| gnomADe | v4.1 |
| gnomADg | v4.1 |
| polyphen | 2.2.3 |
| regbuild | 1.0 |
| sift | 6.2.1 |
General statistics
| Lines of input read | 21626 |
| Variants processed | 21626 |
| Variants filtered out | 0 |
| Novel / existing variants | 0 (0.0) / 21626 (100.0) |
| Overlapped genes | 13077 |
| Overlapped transcripts | 13368 |
| Overlapped regulatory features | 542 |